WHAT IF Check report

This file was created 2013-06-06 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1wdd.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.468
CA-only RMS fit for the two chains : 0.176

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: S and W

All-atom RMS fit for the two chains : 0.593
CA-only RMS fit for the two chains : 0.161

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: S and W

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1172 MME   (   1-)  S  -
1174 CAP   (1001-)  A  -
1193 CAP   (2001-)  E  -
1194 MME   (   1-)  W  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 466 GLN   (   2-)  S  -   N   bound to 1172 MME   (   1-)  S  -   C
1051 GLN   (   2-)  W  -   N   bound to 1194 MME   (   1-)  W  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: W

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: W

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  69 ARG   (  79-)  A

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 525 TYR   (  61-)  S

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 476 PHE   (  12-)  S
 561 PHE   (  97-)  S
1061 PHE   (  12-)  W
1146 PHE   (  97-)  W

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 489 ASP   (  25-)  S
 669 ASP   (  94-)  E
1074 ASP   (  25-)  W

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  18 GLU   (  28-)  A
  83 GLU   (  93-)  A
 328 GLU   ( 338-)  A
 552 GLU   (  88-)  S
 913 GLU   ( 338-)  E
1018 GLU   ( 443-)  E
1137 GLU   (  88-)  W

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 191 KCX   ( 201-)  A      CH     CX
 191 KCX   ( 201-)  A      OX1    OQ1
 191 KCX   ( 201-)  A      OX2    OQ2
 776 KCX   ( 201-)  E      CH     CX
 776 KCX   ( 201-)  E      OX1    OQ1
 776 KCX   ( 201-)  E      OX2    OQ2

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 287 MET   ( 297-)  A      CG   SD    1.96    4.5
 291 ILE   ( 301-)  A      CA   CB    1.63    4.8
 692 PHE   ( 117-)  E      CD1  CE1   1.50    4.0
1036 ILE   ( 461-)  E      CA   CB    1.63    4.9
1161 ILE   ( 112-)  W      CA   CB    1.62    4.6

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.994445 -0.000639 -0.000861|
 | -0.000639  0.994536  0.001069|
 | -0.000861  0.001069  0.993502|
Proposed new scale matrix

 |  0.009002  0.000006  0.000008|
 |  0.000006  0.009001 -0.000010|
 |  0.000004 -0.000005  0.005115|
With corresponding cell

    A    = 111.086  B   = 111.097  C    = 195.494
    Alpha=  89.877  Beta=  90.099  Gamma=  90.074

The CRYST1 cell dimensions

    A    = 111.713  B   = 111.713  C    = 196.780
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1382.648
(Under-)estimated Z-score: 27.404

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  69 ARG   (  79-)  A      CB   CG   CD  106.05   -4.0
  73 ARG   (  83-)  A      CB   CG   CD  104.92   -4.6
 189 PHE   ( 199-)  A      C    CA   CB  101.75   -4.4
 229 TYR   ( 239-)  A      CA   CB   CG  121.85    4.3
 275 ARG   ( 285-)  A      CD   NE   CZ  130.11    4.7
 315 HIS   ( 325-)  A      C    CA   CB  100.36   -5.1
 315 HIS   ( 325-)  A      CA   CB   CG  118.33    4.5
 315 HIS   ( 325-)  A      CB   CG   CD2 134.42    4.1
 317 HIS   ( 327-)  A      CG   ND1  CE1 109.62    4.0
 320 THR   ( 330-)  A      C    CA   CB  102.25   -4.1
 571 ARG   ( 107-)  S      CB   CG   CD  105.76   -4.2
 658 ARG   (  83-)  E      CB   CG   CD  105.83   -4.1
 774 PHE   ( 199-)  E      C    CA   CB  101.39   -4.6
 814 TYR   ( 239-)  E      CA   CB   CG  121.86    4.3
 860 ARG   ( 285-)  E      CD   NE   CZ  129.43    4.3
 900 HIS   ( 325-)  E      C    CA   CB   99.57   -5.5
 900 HIS   ( 325-)  E      CG   ND1  CE1 109.70    4.1
 905 THR   ( 330-)  E      C    CA   CB  102.48   -4.0
1039 ALA   ( 464-)  E     -C    N    CA  114.19   -4.2
1097 GLY   (  48-)  W     -C    N    CA  113.17   -4.4

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  18 GLU   (  28-)  A
  69 ARG   (  79-)  A
  83 GLU   (  93-)  A
 328 GLU   ( 338-)  A
 489 ASP   (  25-)  S
 552 GLU   (  88-)  S
 669 ASP   (  94-)  E
 913 GLU   ( 338-)  E
1018 GLU   ( 443-)  E
1074 ASP   (  25-)  W
1137 GLU   (  88-)  W

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

1169 PRO   ( 120-)  W      N     -8.8   -31.35    -2.48
The average deviation= 1.318

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 914 ARG   ( 339-)  E    5.36
 877 ASP   ( 302-)  E    5.20
 340 ARG   ( 350-)  A    4.75
 292 ASP   ( 302-)  A    4.53
 329 ARG   ( 339-)  A    4.42
 730 ILE   ( 155-)  E    4.36
 655 TYR   (  80-)  E    4.32
 988 ASN   ( 413-)  E    4.19
  70 TYR   (  80-)  A    4.14
 699 VAL   ( 124-)  E    4.13
 844 TYR   ( 269-)  E    4.10

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 143 HIS   ( 153-)  A      CB   5.13
 728 HIS   ( 153-)  E      CB   4.39
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.256

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 519 HIS   (  55-)  S    -2.3
  55 THR   (  65-)  A    -2.2
 640 THR   (  65-)  E    -2.2
 359 VAL   ( 369-)  A    -2.2
1150 ILE   ( 101-)  W    -2.2
 573 VAL   ( 109-)  S    -2.2
 944 VAL   ( 369-)  E    -2.2
 327 GLY   ( 337-)  A    -2.1
1104 HIS   (  55-)  W    -2.1
 912 GLY   ( 337-)  E    -2.1
  65 THR   (  75-)  A    -2.1
1158 VAL   ( 109-)  W    -2.1
 650 THR   (  75-)  E    -2.1
 945 SER   ( 370-)  E    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

 113 ASN   ( 123-)  A  Poor phi/psi
 153 ASN   ( 163-)  A  Poor phi/psi
 162 CYS   ( 172-)  A  Poor phi/psi
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 287 MET   ( 297-)  A  Poor phi/psi
 321 VAL   ( 331-)  A  Poor phi/psi
 360 SER   ( 370-)  A  Poor phi/psi
 477 GLU   (  13-)  S  Poor phi/psi
 479 LEU   (  15-)  S  Poor phi/psi
 501 LYS   (  37-)  S  Poor phi/psi
 534 LYS   (  70-)  S  Poor phi/psi
 637 SER   (  62-)  E  Poor phi/psi
 638 THR   (  63-)  E  Poor phi/psi
 650 THR   (  75-)  E  Poor phi/psi
 670 ASN   (  95-)  E  Poor phi/psi
 698 ASN   ( 123-)  E  Poor phi/psi
 738 ASN   ( 163-)  E  Poor phi/psi
 747 CYS   ( 172-)  E  Poor phi/psi
 750 LYS   ( 175-)  E  PRO omega poor
 782 ASN   ( 207-)  E  Poor phi/psi
 872 MET   ( 297-)  E  Poor phi/psi
 906 VAL   ( 331-)  E  Poor phi/psi
 944 VAL   ( 369-)  E  Poor phi/psi
 945 SER   ( 370-)  E  Poor phi/psi
1062 GLU   (  13-)  W  Poor phi/psi
1064 LEU   (  15-)  W  Poor phi/psi
1086 LYS   (  37-)  W  Poor phi/psi
1119 LYS   (  70-)  W  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.784

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 854 SER   ( 279-)  E    0.35
 803 SER   ( 228-)  E    0.36
 269 SER   ( 279-)  A    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 ALA   (  15-)  A      0
   7 VAL   (  17-)  A      0
   8 LYS   (  18-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  36 PRO   (  46-)  A      0
  51 SER   (  61-)  A      0
  52 SER   (  62-)  A      0
  53 THR   (  63-)  A      0
  56 TRP   (  66-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  73 ARG   (  83-)  A      0
  75 TYR   (  85-)  A      0
  78 GLU   (  88-)  A      0
  81 VAL   (  91-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  86 GLN   (  96-)  A      0
  97 LEU   ( 107-)  A      0
 100 GLU   ( 110-)  A      0
 111 VAL   ( 121-)  A      0
 113 ASN   ( 123-)  A      0
And so on for a total of 439 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 3.897

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 395 GLY   ( 405-)  A   1.55   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 141 PRO   ( 151-)  A    0.46 HIGH
 378 PRO   ( 388-)  A    0.45 HIGH
 951 PRO   ( 376-)  E    0.45 HIGH
1107 PRO   (  58-)  W    0.48 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 625 PRO   (  50-)  E  -116.0 envelop C-gamma (-108 degrees)
 717 PRO   ( 142-)  E   101.4 envelop C-beta (108 degrees)
1169 PRO   ( 120-)  W  -153.5 half-chair N/C-delta (-162 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance; each bump is listed in only one direction,

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1051 GLN   (   2-)  W      N    <->  1194 MME   (   1-)  W      C    1.37    1.33  INTRA B3
 237 CYS   ( 247-)  A      SG   <->   822 CYS   ( 247-)  E      SG   0.92    2.53  INTRA
1051 GLN   (   2-)  W      CA   <->  1194 MME   (   1-)  W      C    0.78    2.42  INTRA
 931 LYS   ( 356-)  E      NZ   <->  1197 HOH   (3356 )  E      O    0.64    2.06  INTRA BF
 670 ASN   (  95-)  E      ND2  <->  1197 HOH   (3315 )  E      O    0.61    2.09  INTRA
1133 LYS   (  84-)  W      NZ   <->  1137 GLU   (  88-)  W      OE2  0.55    2.15  INTRA BF
1175 GOL   (3001-)  A      C1   <->  1195 HOH   (3407 )  A      O    0.42    2.38  INTRA
1195 HOH   (3365 )  A      O    <->  1196 HOH   ( 215 )  S      O    0.38    2.02  INTRA
1074 ASP   (  25-)  W      OD1  <->  1198 HOH   ( 935 )  W      O    0.37    2.03  INTRA BF
1035 GLU   ( 460-)  E      CD   <->  1197 HOH   (3374 )  E      O    0.36    2.44  INTRA BF
1195 HOH   (3299 )  A      O    <->  1195 HOH   (3362 )  A      O    0.36    1.84  INTRA
 948 GLY   ( 373-)  E      N    <->  1190 GOL   (3016-)  E      C1   0.35    2.75  INTRA
1195 HOH   (3085 )  A      O    <->  1197 HOH   (3376 )  E      O    0.35    2.05  INTRA BF
 450 GLU   ( 460-)  A      OE2  <->   453 LYS   ( 463-)  A      NZ   0.35    2.35  INTRA BF
   1 VAL   (  11-)  A      CG1  <->     2 GLY   (  12-)  A      N    0.34    2.66  INTRA BF
1035 GLU   ( 460-)  E      CG   <->  1197 HOH   (3374 )  E      O    0.33    2.47  INTRA BF
1195 HOH   (3299 )  A      O    <->  1195 HOH   (3300 )  A      O    0.33    1.87  INTRA
 177 ARG   ( 187-)  A      NH2  <->  1180 GOL   (3015-)  S      C1   0.31    2.79  INTRA BF
 489 ASP   (  25-)  S      OD1  <->  1196 HOH   ( 192 )  S      O    0.30    2.10  INTRA
1183 GOL   (3002-)  E      O1   <->  1197 HOH   (3375 )  E      O    0.30    2.10  INTRA
1148 ARG   (  99-)  W      NH2  <->  1191 GOL   (3007-)  W      C3   0.30    2.80  INTRA
1195 HOH   (3375 )  A      O    <->  1197 HOH   (3018 )  E      O    0.30    2.10  INTRA BF
1153 ASP   ( 104-)  W      OD1  <->  1155 VAL   ( 106-)  W      CG2  0.29    2.51  INTRA
 731 GLN   ( 156-)  E      OE1  <->  1190 GOL   (3016-)  E      C1   0.27    2.53  INTRA
 436 ARG   ( 446-)  A      O    <->   440 LYS   ( 450-)  A      NZ   0.24    2.46  INTRA
And so on for a total of 132 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 529 TYR   (  65-)  S      -7.87
1114 TYR   (  65-)  W      -7.85
1105 ARG   (  56-)  W      -7.47
 520 ARG   (  56-)  S      -7.36
 464 LYS   ( 474-)  A      -6.37
1049 LYS   ( 474-)  E      -6.31
 139 GLN   ( 149-)  A      -5.98
 706 ARG   ( 131-)  E      -5.95
 724 GLN   ( 149-)  E      -5.92
 470 ILE   (   6-)  S      -5.82
 121 ARG   ( 131-)  A      -5.79
1014 ARG   ( 439-)  E      -5.79
1119 LYS   (  70-)  W      -5.76
 429 ARG   ( 439-)  A      -5.69
   4 LYS   (  14-)  A      -5.63
 534 LYS   (  70-)  S      -5.59
 589 LYS   (  14-)  E      -5.47
1055 ILE   (   6-)  W      -5.43
1052 VAL   (   3-)  W      -5.33
 467 VAL   (   3-)  S      -5.31
  81 VAL   (  91-)  A      -5.31
 538 PHE   (  74-)  S      -5.27
 666 VAL   (  91-)  E      -5.23
 925 ARG   ( 350-)  E      -5.23
 935 ARG   ( 360-)  E      -5.22
 340 ARG   ( 350-)  A      -5.21
1123 PHE   (  74-)  W      -5.21
 350 ARG   ( 360-)  A      -5.19
 184 ARG   ( 194-)  A      -5.12
 862 ASN   ( 287-)  E      -5.11
 277 ASN   ( 287-)  A      -5.10
 769 ARG   ( 194-)  E      -5.04
1008 GLU   ( 433-)  E      -5.03

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: S

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: W

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 289 ALA   ( 299-)  A   -2.82
 874 ALA   ( 299-)  E   -2.79
1158 VAL   ( 109-)  W   -2.73
 573 VAL   ( 109-)  S   -2.69
 680 LEU   ( 105-)  E   -2.58

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: W

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1195 HOH   (3206 )  A      O     51.81   12.34   -6.97
1195 HOH   (3211 )  A      O     28.84   36.34   48.05
1195 HOH   (3217 )  A      O     22.21    0.10   -6.30
1195 HOH   (3220 )  A      O     29.28    4.42    6.67
1195 HOH   (3281 )  A      O     25.84   38.89   52.06
1195 HOH   (3323 )  A      O     26.80   36.70   49.70
1195 HOH   (3324 )  A      O     29.97   35.82   45.72
1195 HOH   (3332 )  A      O     49.88   11.42   19.71
1195 HOH   (3343 )  A      O     51.22   10.34   21.82
1195 HOH   (3351 )  A      O     38.08    9.36   17.34
1195 HOH   (3359 )  A      O     46.27   14.27   15.69
1195 HOH   (3399 )  A      O     57.44   11.39   24.84
1195 HOH   (3417 )  A      O     49.10   12.63   15.80
1196 HOH   ( 196 )  S      O     25.95   69.43  -48.72
1196 HOH   ( 210 )  S      O     28.55   68.13  -53.13
1196 HOH   ( 212 )  S      O     31.20   63.67  -56.15
1196 HOH   ( 213 )  S      O     34.10   62.15  -57.66
1196 HOH   ( 214 )  S      O      9.71   26.73   40.31
1197 HOH   (3258 )  E      O     21.08   25.90  -47.04
1197 HOH   (3272 )  E      O     53.43   47.69    4.87
1197 HOH   (3298 )  E      O     21.34   23.42  -41.54
1197 HOH   (3299 )  E      O     19.44   69.93  -52.83
1197 HOH   (3357 )  E      O      1.34   47.22  -17.74
1198 HOH   ( 676 )  W      O     64.97   31.87   54.16
1198 HOH   ( 747 )  W      O     16.10   29.48  -44.74
1198 HOH   ( 771 )  W      O     63.26   35.15   50.78
1198 HOH   ( 772 )  W      O     61.81   36.73   51.86
1198 HOH   ( 775 )  W      O     12.63   29.64  -44.62
1198 HOH   ( 804 )  W      O     39.97   51.01   37.49
1198 HOH   ( 860 )  W      O     23.26   36.56  -50.71

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1195 HOH   (3329 )  A      O
1195 HOH   (3331 )  A      O
1195 HOH   (3338 )  A      O
1195 HOH   (3345 )  A      O
1195 HOH   (3349 )  A      O
1195 HOH   (3351 )  A      O
1195 HOH   (3367 )  A      O
1195 HOH   (3395 )  A      O
1195 HOH   (3404 )  A      O
1195 HOH   (3405 )  A      O
1195 HOH   (3406 )  A      O
1196 HOH   ( 161 )  S      O
1196 HOH   ( 182 )  S      O
1196 HOH   ( 210 )  S      O
1196 HOH   ( 236 )  S      O
1196 HOH   ( 237 )  S      O
1196 HOH   ( 238 )  S      O
1196 HOH   ( 240 )  S      O
1196 HOH   ( 243 )  S      O
1196 HOH   ( 244 )  S      O
1196 HOH   ( 245 )  S      O
1196 HOH   ( 246 )  S      O
1196 HOH   ( 247 )  S      O
1197 HOH   (3209 )  E      O
1197 HOH   (3258 )  E      O
1197 HOH   (3272 )  E      O
1197 HOH   (3298 )  E      O
1197 HOH   (3299 )  E      O
1197 HOH   (3308 )  E      O
1197 HOH   (3333 )  E      O
1197 HOH   (3336 )  E      O
1197 HOH   (3338 )  E      O
1197 HOH   (3339 )  E      O
1197 HOH   (3357 )  E      O
1197 HOH   (3359 )  E      O
1197 HOH   (3368 )  E      O
1197 HOH   (3371 )  E      O
1197 HOH   (3372 )  E      O
1198 HOH   ( 551 )  W      O
1198 HOH   ( 557 )  W      O
1198 HOH   ( 675 )  W      O
1198 HOH   ( 676 )  W      O
1198 HOH   ( 680 )  W      O
1198 HOH   ( 745 )  W      O
1198 HOH   ( 746 )  W      O
1198 HOH   ( 865 )  W      O
1198 HOH   ( 932 )  W      O
1198 HOH   ( 937 )  W      O
ERROR. No convergence in HB2STD
Old,New value: 1659.535 1659.549

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 317 HIS   ( 327-)  A
 493 GLN   (  29-)  S
 518 ASN   (  54-)  S
 661 HIS   (  86-)  E
 879 GLN   ( 304-)  E
 902 HIS   ( 327-)  E
1017 ASN   ( 442-)  E
1078 GLN   (  29-)  W

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
 133 THR   ( 143-)  A      OG1
 163 THR   ( 173-)  A      OG1
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 195 ASN   ( 205-)  A      ND2
 201 PHE   ( 211-)  A      N
 229 TYR   ( 239-)  A      OH
 236 THR   ( 246-)  A      N
 285 ARG   ( 295-)  A      NE
 313 GLY   ( 323-)  A      N
 356 GLN   ( 366-)  A      NE2
 369 SER   ( 379-)  A      N
 371 GLY   ( 381-)  A      N
 391 GLN   ( 401-)  A      NE2
 394 GLY   ( 404-)  A      N
 403 ASN   ( 413-)  A      ND2
 479 LEU   (  15-)  S      N
 493 GLN   (  29-)  S      NE2
 513 PHE   (  49-)  S      N
 520 ARG   (  56-)  S      NH2
 525 TYR   (  61-)  S      N
And so on for a total of 55 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 282 HIS   ( 292-)  A      NE2
 843 ASP   ( 268-)  E      OD1
 843 ASP   ( 268-)  E      OD2
 867 HIS   ( 292-)  E      NE2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1195 HOH   (3067 )  A      O  1.08  K  4 NCS 1/1
1195 HOH   (3076 )  A      O  0.89  K  5
1196 HOH   ( 192 )  S      O  0.95 CA  6 (or NA)
1197 HOH   (3066 )  E      O  0.93  K  4 NCS 1/1
1197 HOH   (3082 )  E      O  0.99  K  4 NCS 1/1
1197 HOH   (3100 )  E      O  0.94  K  5
1197 HOH   (3142 )  E      O  0.87  K  5 NCS 1/1
1198 HOH   ( 245 )  W      O  0.94  K  4 NCS 1/1
1198 HOH   ( 430 )  W      O  1.06  K  4 NCS 1/1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 150 ASP   ( 160-)  A   H-bonding suggests Asn
 258 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 735 ASP   ( 160-)  E   H-bonding suggests Asn
 843 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.747
  2nd generation packing quality :   0.601
  Ramachandran plot appearance   :  -0.256
  chi-1/chi-2 rotamer normality  :  -0.784
  Backbone conformation          :  -0.800

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.878
  Bond angles                    :   0.958
  Omega angle restraints         :   0.709 (tight)
  Side chain planarity           :   0.763
  Improper dihedral distribution :   1.106
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   1.091

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.35


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.878
  Bond angles                    :   0.958
  Omega angle restraints         :   0.709 (tight)
  Side chain planarity           :   0.763
  Improper dihedral distribution :   1.106
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   1.091
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.